Join objects with procedural material
You would need to make sure all the objects have UVs that do not overlap in the UV space. This way baking will work if all the objects share the same material and are selected.

In order to edit UVs for every leaf you would also need to make their data unique with Make Singe User. You can find it using the search in 2.8, or by going to Object>Relations>Make Single User.

It's also now possible to edit multiple objects at once in 2.8 so it's very easy to unwrap all the leafs to one UV map at once.